[apbs-announce] APBS 1.5 released

[Baker, Nathan]

Dearest APBS users,

We are pleased to announce the latest release of APBS 1.5. The latest version of APBS includes several notable features and bug fixes. This release includes the addition of Poisson-Boltzmann Analytical-Method (PB-AM), Poisson-Boltzmann Semi-Analytical Method (PB-SAM) and the Treecode-Accelerated Boundary Integral Poisson-Boltzmann method (TABI). Additionally, we have made improvements to the build system and the system tests, as well as miscellaneous bug fixes. A full change log may be found here.

For help with installation, building, or running APBS, please visit https://gitter.im/Electrostatics/help.

We thank you for your continued support of APBS.

Sincerely,

The APBS Development Team

 

APBS 1.5 CHANGELOG

These are notes for APBS version 1.5

• Binary releases may be found on GitHub and on SourceForge.

New Features

• Poisson-Boltzmann Analytical Method (PBAM, see Lotan & Head-Gordon) and Semi-Analytical Method (PBSAM, see Yap & Head-Gordon) integrated with APBS. PBSAM is currently only available in the Linux and OS X distributions.
  • Examples are located with the APBS examples in the pbam/ and pbsam/ directories.
  • More information and documentation may be found in the PBAM and PBSAM sections of the APBS-PDB2PQR website.
• Tree-Code Accelerated Boundary Integral Poisson-Boltzmann Method (TABI-PB) integrated with APBS.(See Geng & Krasny)
  • Examples are located with the APBS examples in the bem/, bem-pKa/, and bem-binding-energies/ folders
  • Included NanoShaper alternative to MSMS.
  • More information and documentation may be found in the Contributions section of the APBS-PDB2PQR website
• Added binary DX format support to the appropriate APBS tools.
• Test suite amended and expanded.
• Removed hard-coded limitation to number of grid points used to determine surface accessibility.

Known Bugs / Limitations

• PBSAM not building in windows due to C standard restrictions in the Microsoft compiler implementation.

Bug Fixes

• Build an iAPBS build bug.
• Fixed miscellaneous Windows build issues.
• OS X bundle problem on El Capitan.

Notes

• The following are included in APBS as Git submodules:
• Geometric Flow (link)
• FETk (link)
• PBAM/PBSAM (link)
• TABI-PB (link)
• To build on Windows from source, the root CMakeLists.txt file needs to be modified by un-commenting out the lines after "#if building on Windows" and commenting out the corresponding lines above.

 

 

--

Nathan Baker

Advanced Computing, Mathematics, and Data Division — Pacific Northwest Natl Lab

Division of Applied Mathematics — Brown University

+1-509-375-3997 — http://go.usa.gov/xWY9Y